20-10216813-A-T

Position:

• chr20-10216813-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040710.1(SNAP25-AS1):​n.270+2424T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,468 control chromosomes in the GnomAD database, including 20,672 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (20672 hom., cov: 29)
• Consequence: SNAP25-AS1 NR_040710.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

Genes affected

SNAP25-AS1 (HGNC:44312): (SNAP25 antisense RNA 1)

SNAP25 (HGNC:11132): (synaptosome associated protein 25) Synaptic vesicle membrane docking and fusion is mediated by SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) located on the vesicle membrane (v-SNAREs) and the target membrane (t-SNAREs). The assembled v-SNARE/t-SNARE complex consists of a bundle of four helices, one of which is supplied by v-SNARE and the other three by t-SNARE. For t-SNAREs on the plasma membrane, the protein syntaxin supplies one helix and the protein encoded by this gene contributes the other two. Therefore, this gene product is a presynaptic plasma membrane protein involved in the regulation of neurotransmitter release. Two alternative transcript variants encoding different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNAP25-AS1	NR_040710.1	n.270+2424T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNAP25-AS1	ENST00000421143.6	n.6-19876T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77711 AN: 151350 Hom.: 20663 Cov.: 29

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.559

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.513 AC: 77745 AN: 151468 Hom.: 20672 Cov.: 29 AF XY: 0.518 AC XY: 38304 AN XY: 73966

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.560

Alfa AF: 0.530 Hom.: 2714

Bravo AF: 0.513

Asia WGS AF: 0.542 AC: 1883 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6077690; hg19: chr20-10197461;